[maker-devel] Model training with AED=0.7 made all contigs FAILED

[Lahcen Campbell]

Hi folks,

I would just like some insight into a recent round of MAKER annotation I 
performed and returned back 0 Finished contigs.

The genome is a white fly, which I successfully ran MAKER on initally 
with the first round of "Evidence in", so passing in EST evidence as 
aligned transcript gffs, protein homology evidence etc. The run was 
successful and produced a lot of good quality gene models

Statistics:
            24,613 genes with 49,547 transcripts containing 141130 cds.

Now, I know this count is very high for our species, so in the 2nd round 
(completed running over 1 night due to all contigs failing) I attempted 
to increase the threshold for support, by reducing AED to 0.7 from an 
initial 1. Prior to starting the second round I had trained SNAP on the 
first round results and also ran Augustus separately and  passed this 
via the snaphmm, pred_gff option. Finally I set min protein to be no 
less than 100Aa and set est2genome and prot2genome off to allow for gene 
model refinement.

I checked the run today and all ~8,000 contigs/scaffolds returned as 
FAILED with all having tried to be retried once each.

My initial feeling was, I feared I have just lost my initial set of 
24,613 gene models. I know believe that this won't be the case but Im 
not sure... Can anyone explain what might have happened here and what 
consequences will follow given they all returned as failed ? Have they 
been deleted from the MAKER data store ?

I had capturdD all 1st round MAKER output files (GFF, Fasta files etc) 
before attempting this 2nd round (i.e. 1st round of model training) of 
MAKER .

If I have irrevocably changed the datastore for MAKER and lost those 
genes, might I be able to restore to an earlier point (say back to the 
first round of evidence in gene models) by passing the first MAKER gff 
in as "maker_gff=" / "pred_pass=1" / "model_pass=1" ?

Any advice on this would be much appreciated
Lahcen








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